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<div class="title">batch.hpp</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* and proprietary rights in and to this software, related documentation</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* and any modifications thereto.  Any use, reproduction, disclosure or</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* distribution of this software and related documentation without an express</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">*/</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160; </div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &lt;claragenomics/cudapoa/cudapoa.hpp&gt;</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160; </div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="preprocessor">#include &lt;claragenomics/utils/graph.hpp&gt;</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160; </div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="preprocessor">#include &lt;memory&gt;</span></div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;<span class="preprocessor">#include &lt;vector&gt;</span></div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160;<span class="preprocessor">#include &lt;stdint.h&gt;</span></div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="preprocessor">#include &lt;string&gt;</span></div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;<span class="preprocessor">#include &lt;iostream&gt;</span></div>
<div class="line"><a name="l00022"></a><span class="lineno">   22</span>&#160;<span class="preprocessor">#include &lt;cuda_runtime_api.h&gt;</span></div>
<div class="line"><a name="l00023"></a><span class="lineno">   23</span>&#160; </div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160;<span class="keyword">namespace </span>claragenomics</div>
<div class="line"><a name="l00025"></a><span class="lineno">   25</span>&#160;{</div>
<div class="line"><a name="l00026"></a><span class="lineno">   26</span>&#160; </div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;<span class="keyword">namespace </span>cudapoa</div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;{</div>
<div class="line"><a name="l00029"></a><span class="lineno">   29</span>&#160; </div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160; </div>
<div class="line"><a name="l00034"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html">   34</a></span>&#160;<span class="keyword">struct </span><a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html">Entry</a></div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160;{</div>
<div class="line"><a name="l00037"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">   37</a></span>&#160;    <span class="keyword">const</span> <span class="keywordtype">char</span>* <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">seq</a>;</div>
<div class="line"><a name="l00039"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277">   39</a></span>&#160;    <span class="keyword">const</span> int8_t* <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277">weights</a>;</div>
<div class="line"><a name="l00041"></a><span class="lineno"><a class="line" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712">   41</a></span>&#160;    int32_t <a class="code" href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712">length</a>;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160;};</div>
<div class="line"><a name="l00043"></a><span class="lineno">   43</span>&#160; </div>
<div class="line"><a name="l00045"></a><span class="lineno"><a class="line" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">   45</a></span>&#160;<span class="keyword">typedef</span> std::vector&lt;Entry&gt; <a class="code" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">Group</a>;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160; </div>
<div class="line"><a name="l00049"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudapoa_1_1Batch.html">   49</a></span>&#160;<span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html">Batch</a></div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160;{</div>
<div class="line"><a name="l00051"></a><span class="lineno">   51</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">~Batch</a>() = <span class="keywordflow">default</span>;</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160; </div>
<div class="line"><a name="l00069"></a><span class="lineno">   69</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">add_poa_group</a>(std::vector&lt;StatusType&gt;&amp; per_seq_status,</div>
<div class="line"><a name="l00070"></a><span class="lineno">   70</span>&#160;                                     <span class="keyword">const</span> <a class="code" href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">Group</a>&amp; poa_group) = 0;</div>
<div class="line"><a name="l00071"></a><span class="lineno">   71</span>&#160; </div>
<div class="line"><a name="l00075"></a><span class="lineno">   75</span>&#160;    <span class="keyword">virtual</span> int32_t <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">get_total_poas</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00076"></a><span class="lineno">   76</span>&#160; </div>
<div class="line"><a name="l00078"></a><span class="lineno">   78</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">generate_poa</a>() = 0;</div>
<div class="line"><a name="l00079"></a><span class="lineno">   79</span>&#160; </div>
<div class="line"><a name="l00090"></a><span class="lineno">   90</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">get_consensus</a>(std::vector&lt;std::string&gt;&amp; consensus,</div>
<div class="line"><a name="l00091"></a><span class="lineno">   91</span>&#160;                                     std::vector&lt;std::vector&lt;uint16_t&gt;&gt;&amp; coverage,</div>
<div class="line"><a name="l00092"></a><span class="lineno">   92</span>&#160;                                     std::vector&lt;claragenomics::cudapoa::StatusType&gt;&amp; output_status) = 0;</div>
<div class="line"><a name="l00093"></a><span class="lineno">   93</span>&#160; </div>
<div class="line"><a name="l00102"></a><span class="lineno">  102</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">StatusType</a> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">get_msa</a>(std::vector&lt;std::vector&lt;std::string&gt;&gt;&amp; msa,</div>
<div class="line"><a name="l00103"></a><span class="lineno">  103</span>&#160;                               std::vector&lt;StatusType&gt;&amp; output_status) = 0;</div>
<div class="line"><a name="l00104"></a><span class="lineno">  104</span>&#160; </div>
<div class="line"><a name="l00111"></a><span class="lineno">  111</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">get_graphs</a>(std::vector&lt;DirectedGraph&gt;&amp; graphs,</div>
<div class="line"><a name="l00112"></a><span class="lineno">  112</span>&#160;                            std::vector&lt;StatusType&gt;&amp; output_status) = 0;</div>
<div class="line"><a name="l00113"></a><span class="lineno">  113</span>&#160; </div>
<div class="line"><a name="l00117"></a><span class="lineno">  117</span>&#160;    <span class="keyword">virtual</span> int32_t <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">batch_id</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00118"></a><span class="lineno">  118</span>&#160; </div>
<div class="line"><a name="l00120"></a><span class="lineno">  120</span>&#160;    <span class="keyword">virtual</span> <span class="keywordtype">void</span> <a class="code" href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">reset</a>() = 0;</div>
<div class="line"><a name="l00121"></a><span class="lineno">  121</span>&#160;};</div>
<div class="line"><a name="l00122"></a><span class="lineno">  122</span>&#160; </div>
<div class="line"><a name="l00136"></a><span class="lineno">  136</span>&#160;std::unique_ptr&lt;Batch&gt; <a class="code" href="group__cudapoa.html#ga81951b681c27354e2dbe7933a9f168f3">create_batch</a>(int32_t max_sequences_per_poa,</div>
<div class="line"><a name="l00137"></a><span class="lineno">  137</span>&#160;                                    int32_t device_id,</div>
<div class="line"><a name="l00138"></a><span class="lineno">  138</span>&#160;                                    cudaStream_t stream,</div>
<div class="line"><a name="l00139"></a><span class="lineno">  139</span>&#160;                                    <span class="keywordtype">size_t</span> max_mem,</div>
<div class="line"><a name="l00140"></a><span class="lineno">  140</span>&#160;                                    int8_t output_mask,</div>
<div class="line"><a name="l00141"></a><span class="lineno">  141</span>&#160;                                    int16_t gap_score,</div>
<div class="line"><a name="l00142"></a><span class="lineno">  142</span>&#160;                                    int16_t mismatch_score,</div>
<div class="line"><a name="l00143"></a><span class="lineno">  143</span>&#160;                                    int16_t match_score,</div>
<div class="line"><a name="l00144"></a><span class="lineno">  144</span>&#160;                                    <span class="keywordtype">bool</span> cuda_banded_alignment);</div>
<div class="line"><a name="l00145"></a><span class="lineno">  145</span>&#160; </div>
<div class="line"><a name="l00147"></a><span class="lineno">  147</span>&#160; </div>
<div class="line"><a name="l00148"></a><span class="lineno">  148</span>&#160;} <span class="comment">// namespace cudapoa</span></div>
<div class="line"><a name="l00149"></a><span class="lineno">  149</span>&#160; </div>
<div class="line"><a name="l00150"></a><span class="lineno">  150</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_ab70c94f0a2b161abd8fce03f487c2db1"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab70c94f0a2b161abd8fce03f487c2db1">claragenomics::cudapoa::Batch::~Batch</a></div><div class="ttdeci">virtual ~Batch()=default</div><div class="ttdoc">CudapoaBatch has a custom dtor, so declare ~Batch virtual and give it a default implementation.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_ab807c4b01c2cddcdebb32952df13c0ec"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab807c4b01c2cddcdebb32952df13c0ec">claragenomics::cudapoa::Batch::batch_id</a></div><div class="ttdeci">virtual int32_t batch_id() const =0</div><div class="ttdoc">Return batch ID.</div></div>
<div class="ttc" id="agroup__cudapoa_html_ga81951b681c27354e2dbe7933a9f168f3"><div class="ttname"><a href="group__cudapoa.html#ga81951b681c27354e2dbe7933a9f168f3">claragenomics::cudapoa::create_batch</a></div><div class="ttdeci">std::unique_ptr&lt; Batch &gt; create_batch(int32_t max_sequences_per_poa, int32_t device_id, cudaStream_t stream, size_t max_mem, int8_t output_mask, int16_t gap_score, int16_t mismatch_score, int16_t match_score, bool cuda_banded_alignment)</div><div class="ttdoc">Creates a new CUDA Batch object.</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_ab8564c38982af7716c70b06d029fb277"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#ab8564c38982af7716c70b06d029fb277">claragenomics::cudapoa::Entry::weights</a></div><div class="ttdeci">const int8_t * weights</div><div class="ttdoc">Pointer to array of weight per base in sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:39</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_a7387b746531d4e8ac1e5806ac2824f09"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a7387b746531d4e8ac1e5806ac2824f09">claragenomics::cudapoa::Batch::generate_poa</a></div><div class="ttdeci">virtual void generate_poa()=0</div><div class="ttdoc">Run partial order alignment algorithm over all POAs.</div></div>
<div class="ttc" id="agroup__cudapoa_html_ga8ece5291074f6e07073b797d34ec24d0"><div class="ttname"><a href="group__cudapoa.html#ga8ece5291074f6e07073b797d34ec24d0">claragenomics::cudapoa::StatusType</a></div><div class="ttdeci">StatusType</div><div class="ttdoc">CUDA POA error type.</div><div class="ttdef"><b>Definition:</b> cudapoa.hpp:22</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_ab39956c82d5d5a2d8df1b1695e15d9d2"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#ab39956c82d5d5a2d8df1b1695e15d9d2">claragenomics::cudapoa::Batch::get_msa</a></div><div class="ttdeci">virtual StatusType get_msa(std::vector&lt; std::vector&lt; std::string &gt;&gt; &amp;msa, std::vector&lt; StatusType &gt; &amp;output_status)=0</div><div class="ttdoc">Get the multiple sequence alignments for each POA.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_a8f2f44e7b4d7f51d8ba68323841dcdf0"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a8f2f44e7b4d7f51d8ba68323841dcdf0">claragenomics::cudapoa::Batch::add_poa_group</a></div><div class="ttdeci">virtual StatusType add_poa_group(std::vector&lt; StatusType &gt; &amp;per_seq_status, const Group &amp;poa_group)=0</div><div class="ttdoc">Add a new group to the batch to run POA algorithm on. Based on the constraints of the batch,...</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_af2b27869811283b869700c181a75cfdc"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#af2b27869811283b869700c181a75cfdc">claragenomics::cudapoa::Batch::get_total_poas</a></div><div class="ttdeci">virtual int32_t get_total_poas() const =0</div><div class="ttdoc">Get total number of partial order alignments in batch.</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_a4ada5ced9af7930c95d7a49fb5ecdac4"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#a4ada5ced9af7930c95d7a49fb5ecdac4">claragenomics::cudapoa::Entry::seq</a></div><div class="ttdeci">const char * seq</div><div class="ttdoc">Pointer to string representing sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:37</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html">claragenomics::cudapoa::Batch</a></div><div class="ttdef"><b>Definition:</b> batch.hpp:49</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_aa8de262cb7c43d7219f7064bb700e7ae"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#aa8de262cb7c43d7219f7064bb700e7ae">claragenomics::cudapoa::Batch::reset</a></div><div class="ttdeci">virtual void reset()=0</div><div class="ttdoc">Reset batch. Must do before re-using batch.</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html">claragenomics::cudapoa::Entry</a></div><div class="ttdoc">A structure to represent a sequence entry.</div><div class="ttdef"><b>Definition:</b> batch.hpp:34</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_a3224d1595caa5950c34708f4b7d64fe0"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a3224d1595caa5950c34708f4b7d64fe0">claragenomics::cudapoa::Batch::get_consensus</a></div><div class="ttdeci">virtual StatusType get_consensus(std::vector&lt; std::string &gt; &amp;consensus, std::vector&lt; std::vector&lt; uint16_t &gt;&gt; &amp;coverage, std::vector&lt; claragenomics::cudapoa::StatusType &gt; &amp;output_status)=0</div><div class="ttdoc">Get the consensus for each POA.</div></div>
<div class="ttc" id="astructclaragenomics_1_1cudapoa_1_1Entry_html_a2211688d275c808bf9b4f85336db6712"><div class="ttname"><a href="structclaragenomics_1_1cudapoa_1_1Entry.html#a2211688d275c808bf9b4f85336db6712">claragenomics::cudapoa::Entry::length</a></div><div class="ttdeci">int32_t length</div><div class="ttdoc">Length of sequence.</div><div class="ttdef"><b>Definition:</b> batch.hpp:41</div></div>
<div class="ttc" id="agroup__cudapoa_html_ga6b301a3a6ac7edccc403ec75e7497d32"><div class="ttname"><a href="group__cudapoa.html#ga6b301a3a6ac7edccc403ec75e7497d32">claragenomics::cudapoa::Group</a></div><div class="ttdeci">std::vector&lt; Entry &gt; Group</div><div class="ttdoc">A type defining the set and order of Entry's in which a POA is processed.</div><div class="ttdef"><b>Definition:</b> batch.hpp:45</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudapoa_1_1Batch_html_a0949cca1e89a40d759b0ca371512bb16"><div class="ttname"><a href="classclaragenomics_1_1cudapoa_1_1Batch.html#a0949cca1e89a40d759b0ca371512bb16">claragenomics::cudapoa::Batch::get_graphs</a></div><div class="ttdeci">virtual void get_graphs(std::vector&lt; DirectedGraph &gt; &amp;graphs, std::vector&lt; StatusType &gt; &amp;output_status)=0</div><div class="ttdoc">Get the graph representation for each POA.</div></div>
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